There's a few things to unpack here.
First, the Atlantis theories are essentially racist. Fundamentally, what it does is take some impressive structure--Great Zimbabwe probably the most notorious example--and ask who built it. The natural first place to start looking is among the indigenous inhabitants (and in basically all cases, there is substantial evidence that this is indeed the case), but this theory is instead built by another group of people for whom there is really no evidence. In other words, the theory is going well out of its way to avoid the explanation that the indigenous inhabitants, to such a degree that you have to ask why. And the "why" is probably an inability to believe that the indigenous people could be capable of building such structures.
The second thing to point is the degree of lack of evidence. This isn't "oh, we haven't found any evidence;" no, it's "we have to posit something completely unlike every known explain to explain why we haven't found any hint of evidence." Yes, global sea levels were at lower doing the last glacial maximum--but note that every early civilization we have spread out substantially far from the coastline. Most of them weren't even centered on the coast.
Third, the framing of "just asking questions" and "I'm a journalist, not an archaeologist" is something that just pisses me off. Hancock has been pushing this narrative for several decades now (and the underlying theories are over a century old)--the questions he's asking have already been answered. He's clearly not interested in listening to the answers--and that makes him not even a journalist but a propagandist instead. If he's proven so unwilling to change, we shouldn't give him the benefit of the doubt and pretend that he's some kind of pop psychologist.
And the final, and most frustrating thing is, this sort of stuff sucks the air out of actual interesting archaeology. A great example of pop archaeology that covers "challenges to mainstream archaeology" [1] well is Charles Mann's 1491, which has the benefit of everything being supportable by actual evidence. And it still manages to bring up interesting questions like "what is a writing system?" (is the Andean quipu a writing system?) or "is agriculture a prerequisite for civilization?" (Norte Chico suggests perhaps not). But instead of stuff like that in documentaries, all we get is... Ancient Aliens^H^H^H^H^H^H Atlanteans. Again.
[1] One really unfortunate aspect of pop archaeology is that it's generally stuck in the early 20th century. This means that the current "consensus" in archaeology is actually surprisingly against what people think of "mainstream archaeology."